DCP2 RNA-Seq in K562

General Information


RBP	DCP2
Cell_Line	K562
Method	CRISPR
Exp_Name	DCP2-BGKcLV21-K562
ENCODE_series_ID	ENCSR834MEV
Batch_ID	BGKcLV21
Pool ID	Pool-200928
Local_Set_Name	set45_K
ENCODE_KD_Exp_ID	ENCSR423ERM
ENCODE_CN_Exp_ID	ENCSR854OFV
Rep1	DCP2-BGKcLV21-15
Rep2	DCP2-BGKcLV21-16
CN1	NT-BGKcLV21-1
CN2	NT-BGKcLV21-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	57.4
Rep2_WB	66.4
Antibody Cat#	A302-597A
Antibody Lot#	Lot# 1
Antibody DCC ID	ENCAB319ZUF
Status	Released
Project	ENCODE4
ID	66

Experiment Information (Status: Released)

	BGKcLV21-15	BGKcLV21-16
idx	748	749
TRCN#_or_BGC#	BGC#0000508	BGC#0000508
shRNA_or_gRNA_sequence	CACGCCGGCTAAACCCACTG	CACGCCGGCTAAACCCACTG
PAM
Name	DCP2_90	DCP2_90
Sample_ID	BGKcLV21-15	BGKcLV21-16
transduction_Date	8/4/20	8/4/20
days	Day 6	Day 6
RBP_name	DCP2	DCP2
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	3697	4844
WB_result	57.4	66.4
Ave_WB	61.9
WB_DONE_date	10/21/20
MW	48.4kDa
IP	Rabbit / I
antibody_Cat#	A302-597A	Lot# 1
Antibody DCC ID	ENCAB319ZUF
submitted_to_DCC_date	11/16/20
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	09/24/20	09/24/20
repeat_library
Note
ID	4868	4869

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DCP2	Product_ID: A302-597A Lot_ID: 1 Source: Bethyl Labs Target Name: DCP2-human

Experiment Status

	BGKcLV21-15	BGKcLV21-16
Sample_ID	BGKcLV21-15	BGKcLV21-16
Sample Name
Sample Name	DCP2-BGKcLV21-15	DCP2-BGKcLV21-16
RBP	DCP2	DCP2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	6123	6124

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV21-15	BGKcLV21-16
Sample #	41	42
Sample Name	DCP2-BGKcLV21-15	DCP2-BGKcLV21-16
Sample_Name_Alias
Index Well Position	C05	D05
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-09-24	2020-09-24
Lib_ID	Lib-200924	Lib-200924
Tecan_Location
Tecan
Tecan_date
Size_bp	323	305
Peak_Molarity	289.00	298.00
libSampleQC_DNA_Well	DNA_Library_set45/set1/C5.png	DNA_Library_set45/set1/D5.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_set45/set1/C5.png	RNA_Library_set45/set2/D10.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-09-22	2020-09-22
Sample_ID	BGKcLV21-15	BGKcLV21-16
RBP	DCP2	DCP2
Batch_ID	BGKcLV21	BGKcLV21
WB_result	52.000	55.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	815	816

Sequencing Information

	BGKcLV21-15	BGKcLV21-16
Sample_ID	BGKcLV21-15	BGKcLV21-16
Sample Name	DCP2-BGKcLV21-15	DCP2-BGKcLV21-16
Pool ID	Pool-200928	Pool-200928
LocalServer_folder	set45_K	set45_K
total_reads	172,813,344	127,288,800
total_aligned_reads	170,794,320	121,569,228
unique_aligned_reads	156,373,364	111,023,254
percent_uniqueAligned	0.90487	0.87222
correlation_replicates	0.973366	0.973366
spikein_reads	96,304	62,524
percent_spikeins	0.00056	0.00049
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	446	447

Data Submission Information

	BGKcLV21-15	BGKcLV21-15	BGKcLV21-15	BGKcLV21-15	BGKcLV21-15	BGKcLV21-15	BGKcLV21-16	BGKcLV21-16	BGKcLV21-16	BGKcLV21-16
ENCODE_alias	brenton-graveley:DCP2-BGKcLV21	brenton-graveley:DCP2-BGKcLV21-15	brenton-graveley:L-DCP2-BGKcLV21-15	brenton-graveley:DCP2-BGKcLV21-15_S35_R1_001.fastq.gz	brenton-graveley:DCP2-BGKcLV21-15_S35_R2_001.fastq.gz	brenton-graveley:DCP2-BGKcLV21-K562	brenton-graveley:DCP2-BGKcLV21-16	brenton-graveley:L-DCP2-BGKcLV21-16	brenton-graveley:DCP2-BGKcLV21-16_S36_R1_001.fastq.gz	brenton-graveley:DCP2-BGKcLV21-16_S36_R2_001.fastq.gz
ENCODE_accession	ENCSR423ERM	ENCBS273URR	ENCLB973RYA	ENCFF909JIL	ENCFF528LTU	ENCSR834MEV	ENCBS340MGE	ENCLB874GJR	ENCFF492RGX	ENCFF546EIL
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKcLV21-15	BGKcLV21-15	BGKcLV21-15	BGKcLV21-15	BGKcLV21-15	BGKcLV21-15	BGKcLV21-16	BGKcLV21-16	BGKcLV21-16	BGKcLV21-16
Sample Name	DCP2-BGKcLV21-15	DCP2-BGKcLV21-15	DCP2-BGKcLV21-15	DCP2-BGKcLV21-15	DCP2-BGKcLV21-15	DCP2-BGKcLV21-15	DCP2-BGKcLV21-16	DCP2-BGKcLV21-16	DCP2-BGKcLV21-16	DCP2-BGKcLV21-16
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV45K_biosample_protocol	LV45K_library_protocol				LV45K_biosample_protocol	LV45K_library_protocol
protocol_URL		DCP2-BGKcLV21-15.pdf	L-DCP2-BGKcLV21-15.pdf				DCP2-BGKcLV21-16.pdf	L-DCP2-BGKcLV21-16.pdf
ID	2107	2169	2239	2309	2379	7170	2170	2240	2310	2380

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	platform	read_length	run_type	paired_end	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
DCP2-BGKcLV21-15_S35_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	446	NovaSeq6000	100	paired-ended	1				NT-BGKcLV21-1_S25_R1_001.fastq.gz,NT-BGKcLV21-2_S26_R1_001.fastq.gz	ENCODE4	1218
DCP2-BGKcLV21-15_S35_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	446	NovaSeq6000	100	paired-ended	2				NT-BGKcLV21-1_S25_R2_001.fastq.gz,NT-BGKcLV21-2_S26_R2_001.fastq.gz	ENCODE4	1268
DCP2-BGKcLV21-15_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	446					GRCh38	V40	DCP2-BGKcLV21-15_S35_R1_001.filtered.trimmed.paired.fastq.gz,DCP2-BGKcLV21-15_S35_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25211
DCP2-BGKcLV21-15_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	446					GRCh38	V40	DCP2-BGKcLV21-15_S35_R1_001.filtered.trimmed.paired.fastq.gz,DCP2-BGKcLV21-15_S35_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27165
DCP2-BGKcLV21-15_Signal.Unique.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	446					GRCh38	V40	DCP2-BGKcLV21-15/Aligned.sortedByCoord.out.bam		ENCORE2	27215
DCP2-BGKcLV21-15_Signal.Unique.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	446					GRCh38	V40	DCP2-BGKcLV21-15/Aligned.sortedByCoord.out.bam		ENCORE2	27265
DCP2-BGKcLV21-15_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	446					GRCh38	V40	DCP2-BGKcLV21-15/Aligned.sortedByCoord.out.bam		ENCORE2	27315
DCP2-BGKcLV21-15_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	446					GRCh38	V40	DCP2-BGKcLV21-15/Aligned.sortedByCoord.out.bam		ENCORE2	27365
DCP2-BGKcLV21-16_S36_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	447	NovaSeq6000	100	paired-ended	1				NT-BGKcLV21-1_S25_R1_001.fastq.gz,NT-BGKcLV21-2_S26_R1_001.fastq.gz	ENCODE4	1219
DCP2-BGKcLV21-16_S36_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	447	NovaSeq6000	100	paired-ended	2				NT-BGKcLV21-1_S25_R2_001.fastq.gz,NT-BGKcLV21-2_S26_R2_001.fastq.gz	ENCODE4	1269
DCP2-BGKcLV21-16_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	447					GRCh38	V40	DCP2-BGKcLV21-16_S36_R1_001.filtered.trimmed.paired.fastq.gz,DCP2-BGKcLV21-16_S36_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25212
DCP2-BGKcLV21-16_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	447					GRCh38	V40	DCP2-BGKcLV21-16_S36_R1_001.filtered.trimmed.paired.fastq.gz,DCP2-BGKcLV21-16_S36_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27166
DCP2-BGKcLV21-16_Signal.Unique.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	447					GRCh38	V40	DCP2-BGKcLV21-16/Aligned.sortedByCoord.out.bam		ENCORE2	27216
DCP2-BGKcLV21-16_Signal.Unique.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	447					GRCh38	V40	DCP2-BGKcLV21-16/Aligned.sortedByCoord.out.bam		ENCORE2	27266
DCP2-BGKcLV21-16_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	447					GRCh38	V40	DCP2-BGKcLV21-16/Aligned.sortedByCoord.out.bam		ENCORE2	27316
DCP2-BGKcLV21-16_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	447					GRCh38	V40	DCP2-BGKcLV21-16/Aligned.sortedByCoord.out.bam		ENCORE2	27366